X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fvarna%2FVarnaCommands.java;h=a1d3a778841b0e96c32cee4f0cc299cf99295b71;hp=9d57969d73f3e079823cec21e0f03be6a7bbe2f3;hb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;hpb=1cc81e06ac2faa5ee4b8879e9fa019956e34259f

diff --git a/src/jalview/ext/varna/VarnaCommands.java b/src/jalview/ext/varna/VarnaCommands.java
index 9d57969..a1d3a77 100644
--- a/src/jalview/ext/varna/VarnaCommands.java
+++ b/src/jalview/ext/varna/VarnaCommands.java
@@ -15,31 +15,35 @@ import java.awt.Color;
 import java.util.ArrayList;
 
 /**
- * Routines for generating Jmol commands for Jalview/Jmol binding
- * another cruisecontrol test.
+ * Routines for generating Jmol commands for Jalview/Jmol binding another
+ * cruisecontrol test.
  * 
  * @author JimP
- *
+ * 
  */
 public class VarnaCommands
 {
 
   /**
-   * Jmol utility which constructs the commands to colour chains by the given alignment
+   * Jmol utility which constructs the commands to colour chains by the given
+   * alignment
    * 
    */
-  public static String[] getColourBySequenceCommand(StructureSelectionManager ssm, String[] files, SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr, AlignmentI alignment)
+  public static String[] getColourBySequenceCommand(
+          StructureSelectionManager ssm, String[] files,
+          SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
+          AlignmentI alignment)
   {
     ArrayList<String> str = new ArrayList<String>();
     StringBuffer command = new StringBuffer();
-  
+
     for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
     {
       StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
-  
+
       if (mapping == null || mapping.length < 1)
         continue;
-  
+
       int lastPos = -1;
       for (int s = 0; s < sequence[pdbfnum].length; s++)
       {
@@ -57,14 +61,14 @@ public class VarnaCommands
                 continue;
               }
               int pos = mapping[m].getPDBResNum(asp.findPosition(r));
-  
+
               if (pos < 1 || pos == lastPos)
                 continue;
-  
+
               lastPos = pos;
-  
+
               Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
-  
+
               if (fr != null)
                 col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
               String newSelcom = (mapping[m].getChain() != " " ? ":"
@@ -78,16 +82,19 @@ public class VarnaCommands
                       + col.getGreen()
                       + ","
                       + col.getBlue() + "]";
-              if (command.length()>newSelcom.length() && command.substring(command.length()-newSelcom.length()).equals(newSelcom))
+              if (command.length() > newSelcom.length()
+                      && command.substring(
+                              command.length() - newSelcom.length())
+                              .equals(newSelcom))
               {
                 command = VarnaCommands.condenseCommand(command, pos);
                 continue;
               }
               // TODO: deal with case when buffer is too large for Jmol to parse
               // - execute command and flush
-  
+
               command.append(";");
-              if (command.length()>51200)
+              if (command.length() > 51200)
               {
                 // add another chunk
                 str.add(command.toString());
@@ -111,20 +118,25 @@ public class VarnaCommands
 
   public static StringBuffer condenseCommand(StringBuffer command, int pos)
   {
-  
+
     // work back to last 'select'
-    int p=command.length(),q=p;
-    do {
-      p-=6;
-      if (p<1) { p=0; };
-    } while ((q=command.indexOf("select",p))==-1 && p>0);
-    
-    StringBuffer sb = new StringBuffer(command.substring(0,q+7));
-  
-    command =  command.delete(0,q+7);
-  
+    int p = command.length(), q = p;
+    do
+    {
+      p -= 6;
+      if (p < 1)
+      {
+        p = 0;
+      }
+      ;
+    } while ((q = command.indexOf("select", p)) == -1 && p > 0);
+
+    StringBuffer sb = new StringBuffer(command.substring(0, q + 7));
+
+    command = command.delete(0, q + 7);
+
     String start;
-  
+
     if (command.indexOf("-") > -1)
     {
       start = command.substring(0, command.indexOf("-"));
@@ -133,9 +145,9 @@ public class VarnaCommands
     {
       start = command.substring(0, command.indexOf(":"));
     }
-  
+
     sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
-  
+
     return sb;
   }